Blog

I provide code (with details & description) to download gene sequences from GenBank using R. The code allows the user to obtain sequences for multiple species and save them into the same FASTA file. This is a modification of the code I used in Baliga & Law, 2016 (MPE).

Say you have an R script shared between you and several colleagues. You may not be sure that each user with whom you're collaborating has installed all the packages the script will require. This code below provides an easy way to check whether specific packages are in the default Library. If they are, they're simply loaded. If any packages are missing, they're installed (with dependencies) into the default Library and are then loaded.

I recently completed my final requirement for advancing to PhD candidacy: giving a departmental seminar to outline my proposed dissertation research. It's amazing how something like this can be simultaneously wonderful and frustrating.

As the title suggests, I've started writing a few inquiry-based lab activities with Sarah Baumgart, my partner-in-crime through the SCWIBLES program. Sarah teaches both general biology (10th-11th grade) and anatomy & physiology (11th-12th grade) at Watsonville High School. With her strong background in human anatomy and my training in comparative vertebrate morphology, I feel we will make an excellent team in the classroom.

One activity we plan to implement focuses on Leonardo da Vinci's Vitruvian Man drawing. In this lab, students will get the chance to explore the degree to which body proportions are consistent across a variety of individuals. Students will first take measurements on themselves to determine if they each fit da Vinci's assertion that in the ideal human, the span of an individual's arms are equal to his/her height. The students will then pool their data as a class to determine if this is robust across individuals. They are then encouraged to propose other body proportions they would like to explore and are given the chance to measure other students to test their own hypotheses. I think this lab will not only promote these students to be curious about their own bodies, but will also give me the chance to teach them how to use common computer programs (such as MS Excel) to analyze data.

Another activity I would like to do focuses on the mammalian dive response (or dive reflex). A wide variety of mammals (including humans) demonstrate a physiological response when diving into cold water for extended periods. This response is characterized by apnea, bradycardia, and peripheral vasoconstriction. Together, these effects allow the body to conserve oxygen and ensure a more steady supply of blood to vital organs like the brain. In my undergraduate experience at UC Berkeley, I took part in a lab activity during one of my physiology courses that allowed me to experience this firsthand by "diving" into a dishpan of cold water. For the students at Watsonville, I think Sarah and I will "inquirize" this lab activity to see if students can devise their own experiments to determine what factors trigger the dive response in humans.

Towards the end of this month, I'll begin making appearances in Sarah's classes to run these labs and also generally assist her in teaching. I'm always excited to try something new, but I also have a few concerns. As a TA, my students only had to come to our discussion sections on a voluntary basis. Thus, the students who showed up on a weekly basis were generally the more academically-driven crowd, and were a self-selected group. At Watsonville, this will not be the case. I'm curious to see how well the students will respond to inquiry-based learning given the notion that the students themselves do not necessarily want to be in school -- they're there because they have to be. I feel inquiry-based approaches are probably very effective only in motivated students, and I'm curious to see how we might deal with apathy in the classroom.

In my recent visit to the Horn Lab at CSUF, I got a chance to look at many members of the Stichaeid family. As I was hunting through Dr. Horn's jars for specimens of monkeyface prickleback (Cebidichthys violaceus), I noticed how easy it is to confuse this species with the black prickleback (Xiphister atropurpureus). As such, I figured I would dedicate a post to highlight the differences between the two species' morphologies so that anglers (and fellow lab researchers!) can better tell what exactly they're handling. If you're into game fishing and would like to know how to tell your black pricklebacks from your monkeyfaces, this post is for you.

Why So Difficult?
Why is it so hard to tell these two species apart? Just look at the photo below. Both the black prickleback and the monkeyface prickleback are highly-elongate, intertidal crevice-dwelling fishes with similar coloration patterns. Both have terminal mouths with large, fleshy lips and have dorsal and anal fins that seem to be almost continuous with their caudal fins. Plus, it doesn't help that they have overlapping ranges along the Pacific coast, especially along California.

Upon first inspection, the black (left) and monkeyface (right) pricklebacks look almost identical.

Can you tell them apart based on their tails?

Clue #1: Pectoral Fin Size
Quite possibly the easiest and quickest way to differentiate between the two species is to examine the pectoral fins. The black prickleback's pectoral fins are quite reduced, looking like minute flaps compared to those of the monkeyface prickleback.

The black prickleback's (left) pectoral fins are quite reduced in size when compared to those of the monkeyface prickleback (right).

Clue #2: Fleshy Lump and Head Shape
The monkeyface prickleback has a characteristic fleshy lump of fatty tissue that occupies the top of head, a trait that is absent in the black prickleback. As a result, the monkeyface prickleback seems to have a more rounded cranial shape than its torpedo-like cousin.

The monkeyface prickleback (top) has a characteristic fleshy lump on its head, a traitwhich is absent in its cousin, the black prickleback (bottom).

Clue #3: Dorsal Ray Spines
Although I do not have a picture to show for this one, take my word for it: this is another easy way to differentiate the two. Run your fingers along the dorsal fin of your fish. If it feels spiny, it's probably the black prickleback. The monkeyface prickleback has no spines in its dorsal fin -- just soft fin rays -- and is much softer to the touch. You'll have a much easier time grabbing hold of a monkeyface prickleback than a black prickleback.

One of my ongoing sideprojects involves understanding the cranial morphology of the monkeyface prickleback, Cebidichthys violaceus. This species is found along the Pacific coast, ranging from Oregon to Baja California, and inhabiting rocky intertidal and tidepool habitats. Commonly confused with being a type of eel (it's even known as the monkeyface eel), this species is actually a member of Stichaeidae, a family found in the Perciform order. Famous for their distinct, lumpy foreheads, these fish are often caught by anglers using a method called "poke-poling".

A face only a mother could love: a rather large specimen of monkeyface prickleback (Cebidichthys violaceus).

In my ongoing quest to know more about this local species, I came across the work of Dr. Michael Horn, of Cal State Fullerton (CSUF), who has spent much of his life documenting the dietary trends of the Stichaeids of the California coast. In particular, Horn noted that the monkeyface prickleback undergoes a dramatic shift in diet over ontogeny: it goes through a carnivorous stage as a juvenile before making a transition to herbivory as it grows longer than 45mm standard length. A series of papers from the 2000s by Horn and colleagues highlight the fascinating trends in gut morphology and enzymatic activity of this Stichaeid.

This summer, Dr. Horn was kind enough to invite me to his lab at CSUF so that I may view his collection of monkeyface pricklebacks. He has quite a large collection of Stichaeids caught from tidepools, with some jars dating back to the early '70s. I learned a lot from this experience, especially when it comes to eying the subtle differences between C. violaceus and its close cousin Xiphister atropurpureus, the black prickleback (which I will highlight in my next post).

San Simeon, CA seems to be a pretty good site to find monkeyface pricklebacks.

Monkeyface measuring!

This black prickleback doesn't look too happy to have been stuck in a jar of ISO for the last 30 years. Also, I think he looks a little bit like Jason Segal.

In my ongoing quest to obtain specimens for my dissertation research, I managed to find my way to the world's largest collection of fishes: the Smithsonian Institution's National Museum of Natural History (NMNH). The Division of Fishes works tirelessly to collect and catalogue marine & freshwater fishes from around the world. Their collection contains over 24,000 of the roughly 32,000 recognized species of fish worldwide. This collection is so large, that only 35% of the estimated 6.2 million individual specimens have been computer cataloged. Fortunately for me, their efforts are currently focused on obtaining and cataloging Caribbean and Indo-Pacific fishes. These geographic areas are home to the many wrasses, gobies, (marine) angelfishes, and damselfishes that I am analyzing for my dissertation work. As I fortuitously found myself on the East Coast thanks to a good friend's wedding, I decided to visit the NMNH during the same trip. In this visit, I was able to fill in many of the gaps in my current collection (which consists of specimens borrowed from the Cal Academy and the LACM, bought (and euthanized) from the pet trade, and generously donated by Dr. Peter Wainwright).

The Division of Fishes does not reside in Washington D.C. (where the NMNH is), but is actually located a short train-ride away in Suitland, Maryland. The collection is housed in the Museum Support Center, pictured below.

The Smithsonian Institution's Museum Support Center, located in Suitland, Maryland

Similar to how things are set up at the CAS and LACM, the Division of Fishes' collection is set up like an academic library, with rows of specimens organized by family.

At least four of the rows pictured here are dedicated to wrasses (Family: Labridae).

Just a few hundred jars of specimens. No big deal.

The friendly staff of the Division of Fishes were kind enough to set me up in my own office, dedicated to visiting researchers. I gathered that the Division hosts about 150 visitors per year, which probably keeps them quite busy, so I appreciated their hospitality.

My workstation for the day. Comfy chair!

No Escort Required.

Some of these jars date back to the late 1800s. The fish inside smelled quite lovely...

It's easy to see the drastic changes in coloration over ontogeny in Labroides bicolor,
the bicolor (cleaner) wrasse. The juvenile form (L) presents with a
dark lateral stripe; the adult (R) develops darker coloration over the
anterior half of its body. Does anything else change? I'll be able to
answer that question in a few months.

Labroides bicolor: juvenile (L) and adult (R)

We see another obvious transition in Thalassoma lutescens (the
yellow-brown wrasse): there's a huge distinction in coloration between
juveniles (L) and terminal adult males (R). This species cleans
predominately as juveniles, and shifts to eating crabs, molluscs, and
shrimps as adults. Are these transitions in color pattern and diet
accompanied by transitions in musculoskeletal morphology?

Thalassoma lutescens: juveniles (L), terminal adult male (R)

More pictures, you say? Sure, why not?

I always have fun photographing Gomphosus varius, the bird wrasse.

More Thalassoma lutescens

Just the right sizes of Halichoeres argus to borrow for my work.

I'm quite happy with what I gained from this visit -- the specimens I have requested to use for my work should be shipped to me within a few months. I'll be able to make a lot progress over this summer and gather valuable data for my proposal defense, which I'm planning to hold in the fall. I had a blast talking with the staff of the Division of Fishes, and I am grateful for their support of my research. I always enjoy making visits to museum collections, and this one was no exception.

Since my parents live in southern California, I figured I'd make the most of my Spring Break by scheduling a visit to the Ichthyology-Herpetology department at the LA County Museum of Natural History (LACM). In this visit, I had the pleasure of meeting the Collections Manager (and all-around great guy), Rick Feeney. Very much like the Cal Academy, the LACM houses many, many specimens that are organized in shelves -- reminiscent of most libraries. According to Rick, the collection contains over 5 million specimens.

Each of these rows contains hundreds of jars of fish specimens.

You're not a true ichthyologist unless you come up with jokes like this.

Found this little gem lying around. Quality entertainment!

In my ongoing quest to build ontogenetic series for Labrid fishes, I took advantage of the LACM's beautiful collection. Rick Feeney was quite generous with the number of specimens he was willing to loan to me -- he let me get away with 91 little fishies. Here are the spoils!

First up, we have Thalassoma bifasciatum, also known as the bluehead wrasse. This Caribbean species is probably most well-known for being a protogynous hermaphrodite, although many other wrasses exhibit this condition as well. Thus, the largest individuals in a population tend to be terminal-phase males, who exhibit a distinct coloration. If they leave or die, large females will often change sex secondarily. Bluehead wrasses often eat zooplankton and small benthic crustaceans, but can also consume echinoderms and molluscs. This species is also a facultative (juvenile) cleaner of ectoparasites.

A size series of Thalassoma bifasciatum (LACM 54098-040).

Next, we have Halichoeres bivittatus. I already have a few specimens of this species from the Cal Academy, which I highlighted in a previous post. Another protogynous hermaphrodite from the Atlantic, this species also forms leks during breeding. Also unlike T. bifasciatum, this species can undergo sex reversal. Whether any of this helped inspire the common name of "slippery dick wrasse" is a mystery to me. Anyway, this species is a gastropod-eater and occasional piscivore. As I mentioned before, this species is also a facultative (juvenile) cleaner!

These weird fellows below are specimens of Gomphosus varius, the bird wrasse. This Indo-Pacific species uses its elongate jaws to pick off small benthic invertebrates from coral or rocky crevices. Interestingly, this species does not clean, even though it possesses jaws that are conducive to a "picking" feeding mode. I guess it goes to show that there's a lot more to cleaning than having (presumably) adequate morphology -- behavioral ecology plays a huge role in determining the evolutionary trajectory of mutualistic behavior.

Size series of Gomphosus varius (LACM 57407-001).

Some more specimens of Gomphosus varius (LACM 37434-005).

Another familiar face: Halichoeres nicholsi, the spinster wrasse. This facultative (juvenile) species is found in the eastern Pacific. Although it may be hard to really notice by looking at faded museum specimens, this species has very distinct coloration patterns for the juvenile and adult phases. Juveniles have a more blotchy/spotted coloration whereas adults are more uniform in color with a broad bar behind the head.

A size series of Halichoeres nicholsi (LACM 32499-027).

Two juvenile specimens of Halichoeres nicholsi (LACM 43924-005).

The tubelip wrasse, Labrichthys unilineatus, is the most closely-related non-cleaning species to the obligate Labroides and facultative Labropsis cleaners in Labridae. Members of this monophyletic group, called the "labrichthynes", are known for having tube lips. Unlike its sister taxa, L. unilineatus does not clean, and instead feeds on coral polyps.

A few specimens of Labrichthys unilineatus (LACM 42489-026).

Back to the world of Thalassoma: next we have Thalassoma hardwicke. This species, known as the sixbar wrasse for its characteristic stripes, can be found in the Indo-Pacific. It is not a cleaner, but rather a benthic invertivore.

The final species I will highlight tonight is Halichoeres dispilus, the chameleon wrasse. Found in the eastern Pacific, this species feeds on benthic and pelagic invertebrates, but is not a cleaner. Large individuals have been observed to be piscivorous.

A size series of Halichoeres dispilus (LACM 8104-000).

More specimens of Halichoeres dispilus (also from LACM 8104-000).

Two additional juveniles of Halichoeres dispilus (LACM 43822-001).

I was fortunate enough to be able to borrow all of the specimens I have shown here, plus a few more. Much to my delight, Rick Feeney was fine with having me clear & stain these specimens, which is a pretty tall order. As such, I am very thankful to Rick and the rest of the staff at the Museum of Natural History. They run an amazing Ichthyology-Herpetology department, and made me feel very welcome working there for the day.

A great group of folks -- the Ichthyology-Herpetology staff at the LA County Museum of Natural History.

I'm starting to build my collection of specimens from museum loans and pet trade purchases, and I thought I'd share a few photos. I'm interested in building an ontogenetic series for each of the species I show here (and many more), so I can better understand how morphological traits may change over ontogeny. This will help me understand how ontogenetic shifts in morphology, and thus feeding mechanics, may be associated with ontogenetic shifts in diet. I'm looking to have at least 15 specimens per series, so each of the pictures shown here represents a work in-progress.

(Photos after the jump.)

First up: Halichoeres bivittatus, commonly known as the slippery dick wrasse. This species is an eater of gastropods, crabs and other benthic invertebrates as an adult, but is also known to exhibit cleaning behavior as an early juvenile. This Caribbean species is thus a facultative (juvenile) cleaner.

Halichoeres bivittatus

H. bivittatus, smallest

H. bivitatus

H. bivittatus

H. bivitattus, largest (so far)

Next up, we have Halichoeres nicholsi, commonly known as the spinster wrasse. Early juveniles of this species exhibit cleaning behavior, and often form aggregations. As they transition adulthood, members of this species tend to become a bit more solitary, and feed on gastropods, sea urchins and crabs. Thus, this species can be classified as a facultative (juvenile) cleaner.

Halichoeres nicholsi

Unfortunately, the smallest specimen of H. nicholsi I currently have is close to 10cm TL. Individuals of this size or larger rarely (if ever) clean.

H. nicholsi

The largest H. nicholsi I have is roughly half the maximum size of this species.

H. nicholsi -- nasty, big, pointy TEETH!

Here we have Halichoeres nigrescens, the dusky rainbowfish -- another facultative (juvenile) cleaner. Like many other wrasses, this species is a generalist invertivore. Small individuals, however, have been observed to clean other fishes.

Halichoeres nigrescens

At such a small size, this specimen of H. nigrescens probably partakes in cleaning.

H. nigrescens

H. nigrescens

My largest specimen of H. nigrescens seems to be much more deep-bodied than the others. At a TL of just under 7.5 cm, this individual probably no longer cleaned.

My next series, composed of individuals of Halichoeres argus, unfortunately does not show a very broad range in size. Also known as the peacock wrasse or argus wrasse, this species can actually grow up to 12 cm SL. Unlike the other Halichoeres species I currently possess, H. argus is not a cleaner at any point in ontogeny and is a generalist invertivore.

Halichoeres argus

Halichoeres argus

H. argus

H. argus

H. argus

H. argus

We'll depart from the world of Halichoeres and enter the realm of Thalassoma. Below is Thalassoma duperrey, known as the saddleback wrasse. This Hawaiian species is facultative throughout ontogeny, meaning that cleaning behavior has been observed in both juveniles and adults. The majority of its diet, however, is composed of benthic crustaceans and molluscs.

Thalassoma duperrey. Note: specimen 4 is not as deep-bodied as it may seem; a bend in the specimen caused it to curve towards the camera lens, causing distortion.

Thalassoma duperrey

Thalassoma duperrey

Our final species is Thalassoma lutescens, also known as the yellow-brown wrasse, the green moon wrasse, the sunset wrasse, the parrotfish (not to be confused with scarids), the yellow wrasse, and the whistling daughter (my favorite). This species is a facultative (juvenile) cleaner: adults mainly feed on crabs, gastropods and sea urchins and do not partake in cleaning.

A pretty lopsided size series of Thalassoma lutescens.

T. lutescens

T. lutescens

T. lutescens

My largest specimen of Thalassoma lutescens is actually about half the maximum size reported in the literature for this species. Note that this large specimen lacks the dark lateral stripes that the smaller specimens have.

A closer look at my largest specimen of Thalassoma lutescens.

I hope you've enjoyed this post! It's a shame that preserved museum specimens often appear more drab than fresh specimens from the wild. Species in Halichoeres and Thalassoma are quite often characterized by vivid yellows, reds and greens, and it is partially for this reason that these genera are among my favorites. For more on the species I've mentioned here, be sure to check out resources such as FishBase, the EOL, and Arkive.

With my mind set on re-applying for the NSF Predoctoral Fellowship this coming fall, I've devoted a chunk of this summer to gathering preliminary data and organizing the framework of my dissertation. Quite fortunately, the California Academy of Sciences, in Golden Gate Park, San Francisco, boasts one of the largest ichthyology collections in the world. Upon perusing the online database for the Ichthyology collection, I found that many of the taxa I was interested in were housed in this museum! Thanks to the generosity of Senior Collections Manager Dave Catania and Curatorial Assistant Mysi Hoang, I have been able to visit the Cal Academy and get a behind-the-scenes look at the Ichthyology department.

As of now, I have made four visits to the Cal Academy. Each time, I've been allowed to walk in through the Research & Staff Entrance located on the southern face of the building.

The back entrance

The Ichthyology collection at the Cal Academy contains nearly 1.2 million specimens of close to 11,000 distinct species. These specimens, preserved in roughly 200,000 jars, are housed in rows that roughly resemble the layout of a typical library. These rows are organized by family, with each family occupying a distinct "group number".

One of many, many, many rows of specimens

Each of these jars contains at least one specimen, though many contain multiple. Some jars are even filled with close to 50 specimens! Each jar is meticulously labelled with all the pertinent information about the specimen(s): species name, location of collection, date collected, method of preservation...etc. These specimens are preserved beautifully, and some are quite old.

This specimen of Embiotoca jacksoni dates back to 1915!

As I am gathering preliminary data, all of my measurements thus far have been non-invasive. Each time I visit the collection, I load up a cart full of jars and return to my workspace to perform these measurements.

This is my game face.

My visits to the Cal Academy have been extremely rewarding to both my research plans and my personal sense of curiosity. I am eternally grateful to the folks in the Ichthyology department for their guidance and their willingness to foster the hopes of a young scientist!

This marks my first quarter as a TA. It's a interesting feeling -- after going through 4.5 years of undergrad, you get a bit of a "culture shock" when you find yourself on the other side of the classroom. You begin to realize it's your responsibility to ensure that the students in your section actually understand the material. You become personally invested in their successes and failures. It can be quite frustrating at times, especially when you feel as though you're speaking to empty seats. On occasion you even think, "What the hell am I doing up here?" For the most part, however, it's been quite rewarding. I seem to be connecting well with my students, and the strength of this link is reflected in their test scores.

I was a bit nervous before leading my first "discussion" section. I'd kept debating whether I'd wanted to be "the stern taskmaster" or more of a "buddy" figure. I can't even begin to count the number of ways I'd practiced introducing myself in my head. Of course, the way things actually panned out was nothing akin to how I'd planned. It's funny -- you spend so much of your time crafting your approach, but when push comes to shove, all of that falls by the wayside. When I walked up to the blackboard that first time, my mind went blank. I didn't have the presence of mind to tailor my words one way or another -- I just spoke in the manner in which I always do.

For me, this approach seems to work. It's all a matter of communicating effectively to your audience. The most effective way to do this is to be yourself. I've stopped caring about how funny or entertaining I come across -- some days I'm "on" and some days I'm not. The only thing that matters is my students' successes; I've become quite possessive of them.

Although it's only been a few weeks, I've come up with a few guidelines for myself when it comes to teaching:

Be honest. Don't try to be an actor -- people can tell when you're not being genuine.

Don't expect everyone to talk. Some people are naturally quiet and have other ways of expressing themselves.

Encourage students to work together in groups. Students sometimes have difficulty discussing ideas with people in "authoritative" positions. Working together with peers helps resolve these issues.

If attendance is voluntary, appreciate the students who actually show up.

Be prepared to repeat your explanations many, many, many times.

Offer your help even when students don't explicitly ask for it. They may be too shy to approach you and/or may not even realize they're doing something incorrectly.